Are there specific folders that SpiderOak will not sync?

In general, SpiderOak will synchronize any folder that it can back up (including network drives, external drives, USB Keys, and so on).

However, there are some folders we do not recommend synchronizing, such as application data folders. The reason for this is that many applications, such as iTunes and iCal, cannot handle having another process change their data files. For example, you can synchronize your actual music files without any problems, but you shouldn't synchronize the iTunes database of songs.